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LSD2_SCHPO
ID   LSD2_SCHPO              Reviewed;        1273 AA.
AC   Q10135; Q9USA2;
DT   01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1996, sequence version 1.
DT   03-AUG-2022, entry version 139.
DE   RecName: Full=Lysine-specific histone demethylase 2;
DE            EC=1.-.-.-;
GN   Name=lsd2; Synonyms=saf140, swm2; ORFNames=SPAC23E2.02;
OS   Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC   Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC   Schizosaccharomyces.
OX   NCBI_TaxID=284812;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=972 / ATCC 24843;
RX   PubMed=11859360; DOI=10.1038/nature724;
RA   Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA   Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA   Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA   Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA   Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA   Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA   Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA   Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA   O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA   Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA   Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA   Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA   Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA   Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA   Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA   Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA   Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA   Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA   Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA   Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA   del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA   Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA   Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA   Nurse P.;
RT   "The genome sequence of Schizosaccharomyces pombe.";
RL   Nature 415:871-880(2002).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 201-404, AND SUBCELLULAR
RP   LOCATION.
RC   STRAIN=ATCC 38364 / 968;
RX   PubMed=10759889; DOI=10.1046/j.1365-2443.2000.00317.x;
RA   Ding D.-Q., Tomita Y., Yamamoto A., Chikashige Y., Haraguchi T.,
RA   Hiraoka Y.;
RT   "Large-scale screening of intracellular protein localization in living
RT   fission yeast cells by the use of a GFP-fusion genomic DNA library.";
RL   Genes Cells 5:169-190(2000).
RN   [3]
RP   FUNCTION, INTERACTION WITH LSD1, AND SUBCELLULAR LOCATION.
RX   PubMed=16990277; DOI=10.1074/jbc.m606349200;
RA   Nicolas E., Lee M.G., Hakimi M.-A., Cam H.P., Grewal S.I.S.,
RA   Shiekhattar R.;
RT   "Fission yeast homologs of human histone H3 lysine 4 demethylase regulate a
RT   common set of genes with diverse functions.";
RL   J. Biol. Chem. 281:35983-35988(2006).
RN   [4]
RP   SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX   PubMed=16823372; DOI=10.1038/nbt1222;
RA   Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S.,
RA   Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S.,
RA   Yoshida M.;
RT   "ORFeome cloning and global analysis of protein localization in the fission
RT   yeast Schizosaccharomyces pombe.";
RL   Nat. Biotechnol. 24:841-847(2006).
RN   [5]
RP   FUNCTION, IDENTIFICATION IN THE SWM HISTONE DEMETHYLASE COMPLEX, AND
RP   INTERACTION WITH LSD1.
RX   PubMed=17434129; DOI=10.1016/j.molcel.2007.02.023;
RA   Lan F., Zaratiegui M., Villen J., Vaughn M.W., Verdel A., Huarte M.,
RA   Shi Y., Gygi S.P., Moazed D., Martienssen R.A., Shi Y.;
RT   "S. pombe LSD1 homologs regulate heterochromatin propagation and
RT   euchromatic gene transcription.";
RL   Mol. Cell 26:89-101(2007).
RN   [6]
RP   IDENTIFICATION IN THE SWM HISTONE DEMETHYLASE COMPLEX, AND FUNCTION OF THE
RP   SWM COMPLEX.
RX   PubMed=17440621; DOI=10.1371/journal.pone.0000386;
RA   Opel M., Lando D., Bonilla C., Trewick S.C., Boukaba A., Walfridsson J.,
RA   Cauwood J., Werler P.J., Carr A.M., Kouzarides T., Murzina N.V.,
RA   Allshire R.C., Ekwall K., Laue E.D.;
RT   "Genome-wide studies of histone demethylation catalysed by the fission
RT   yeast homologues of mammalian LSD1.";
RL   PLoS ONE 2:E386-E386(2007).
CC   -!- FUNCTION: Catalytic component of the SWM histone demethylase complex
CC       that specifically demethylates H3K9me2, a specific tag for epigenetic
CC       transcriptional activation, thereby acting as a corepressor. Acts by
CC       oxidizing the substrate by FAD to generate the corresponding imine that
CC       is subsequently hydrolyzed. Has a role in regulating heterochromatin
CC       propagation and euchromatic transcription. Also has a gene activating
CC       role. {ECO:0000269|PubMed:16990277, ECO:0000269|PubMed:17434129,
CC       ECO:0000269|PubMed:17440621}.
CC   -!- COFACTOR:
CC       Name=FAD; Xref=ChEBI:CHEBI:57692;
CC   -!- SUBUNIT: Component of the SWM histone demethylase complex composed of
CC       at least lsd1, lsd2, phf1 and phf2. Interacts directly with lsd1.
CC       {ECO:0000269|PubMed:16990277, ECO:0000269|PubMed:17434129,
CC       ECO:0000269|PubMed:17440621}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00267,
CC       ECO:0000269|PubMed:10759889, ECO:0000269|PubMed:16823372,
CC       ECO:0000269|PubMed:16990277}.
CC   -!- SIMILARITY: Belongs to the flavin monoamine oxidase family.
CC       {ECO:0000305}.
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DR   EMBL; CU329670; CAA93114.1; -; Genomic_DNA.
DR   EMBL; AB027920; BAA87224.1; -; Genomic_DNA.
DR   PIR; T38292; T38292.
DR   RefSeq; NP_592937.1; NM_001018338.2.
DR   AlphaFoldDB; Q10135; -.
DR   SMR; Q10135; -.
DR   BioGRID; 278323; 6.
DR   STRING; 4896.SPAC23E2.02.1; -.
DR   iPTMnet; Q10135; -.
DR   MaxQB; Q10135; -.
DR   PaxDb; Q10135; -.
DR   PRIDE; Q10135; -.
DR   EnsemblFungi; SPAC23E2.02.1; SPAC23E2.02.1:pep; SPAC23E2.02.
DR   GeneID; 2541832; -.
DR   KEGG; spo:SPAC23E2.02; -.
DR   PomBase; SPAC23E2.02; lsd2.
DR   VEuPathDB; FungiDB:SPAC23E2.02; -.
DR   eggNOG; KOG0029; Eukaryota.
DR   HOGENOM; CLU_274764_0_0_1; -.
DR   InParanoid; Q10135; -.
DR   OMA; KMQWHVC; -.
DR   PhylomeDB; Q10135; -.
DR   BRENDA; 1.14.11.65; 5613.
DR   PRO; PR:Q10135; -.
DR   Proteomes; UP000002485; Chromosome I.
DR   GO; GO:0000785; C:chromatin; IDA:PomBase.
DR   GO; GO:0005829; C:cytosol; HDA:PomBase.
DR   GO; GO:0033193; C:Lsd1/2 complex; IDA:PomBase.
DR   GO; GO:0005634; C:nucleus; HDA:PomBase.
DR   GO; GO:0003677; F:DNA binding; ISM:PomBase.
DR   GO; GO:0140683; F:histone H3-di/monomethyl-lysine-9 demethylase activity; IDA:PomBase.
DR   GO; GO:0016491; F:oxidoreductase activity; IBA:GO_Central.
DR   GO; GO:0006338; P:chromatin remodeling; IMP:PomBase.
DR   GO; GO:0033696; P:heterochromatin boundary formation; IPI:PomBase.
DR   GO; GO:0016570; P:histone modification; IEA:UniProt.
DR   Gene3D; 1.10.10.10; -; 1.
DR   Gene3D; 1.10.30.10; -; 1.
DR   Gene3D; 3.50.50.60; -; 2.
DR   InterPro; IPR002937; Amino_oxidase.
DR   InterPro; IPR036188; FAD/NAD-bd_sf.
DR   InterPro; IPR009071; HMG_box_dom.
DR   InterPro; IPR036910; HMG_box_dom_sf.
DR   InterPro; IPR009057; Homeobox-like_sf.
DR   InterPro; IPR007526; SWIRM.
DR   InterPro; IPR036388; WH-like_DNA-bd_sf.
DR   Pfam; PF01593; Amino_oxidase; 1.
DR   Pfam; PF04433; SWIRM; 1.
DR   SUPFAM; SSF46689; SSF46689; 1.
DR   SUPFAM; SSF47095; SSF47095; 1.
DR   SUPFAM; SSF51905; SSF51905; 1.
DR   PROSITE; PS50118; HMG_BOX_2; 1.
DR   PROSITE; PS50934; SWIRM; 1.
PE   1: Evidence at protein level;
KW   Chromatin regulator; Coiled coil; DNA-binding; FAD; Flavoprotein; Nucleus;
KW   Oxidoreductase; Reference proteome; Repressor; Transcription;
KW   Transcription regulation.
FT   CHAIN           1..1273
FT                   /note="Lysine-specific histone demethylase 2"
FT                   /id="PRO_0000116463"
FT   DOMAIN          394..490
FT                   /note="SWIRM"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00247"
FT   DNA_BIND        1115..1195
FT                   /note="HMG box"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00267"
FT   REGION          199..237
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          542..1198
FT                   /note="Demethylase activity"
FT                   /evidence="ECO:0000250"
FT   REGION          571..596
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1215..1273
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COILED          247..307
FT                   /evidence="ECO:0000255"
FT   COILED          681..767
FT                   /evidence="ECO:0000255"
FT   COMPBIAS        1215..1263
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         509..551
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000255"
FT   BINDING         517
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         550
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         558
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         572..573
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         1147
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         1156..1157
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   CONFLICT        248
FT                   /note="S -> P (in Ref. 2; BAA87224)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   1273 AA;  142490 MW;  3FEFF6433DF3C0B6 CRC64;
     MPLGRSSWIC CAKYFVNTKS RFNEILPPRF TLIVSFYSMN TSENDPDGHY DFPEMTEHHS
     DRASSYANAN NVNSTQPQLV SSEQALLAIL GGGLQSITPN SVNQNAYSRS TYRTDGGLNS
     QPVSSLNNQW GNYNPAFLPS RYDSSFHPYT ISQAANQPFP QHLLGNSNAG VAQQSGMRTI
     GLPPTVGSSF PQQKSSTYEN FFDANSPSSQ QFPSTYPSRS QNPLSSSGDG STAIHAGPIQ
     HQNSNAFSNY PYPLDASHLS SQQLLSMYRD QVSHGVTPST FRNHESFMPT QLVSATELSK
     SVDNAVLPIP PTTAPAVVSP PASSFPLMSS AATSGNISSP ALFDSELGAR PEGSVAIEPS
     RVLLQWSSQS SSHTIPSAGA SIPTSSLKSF FEHAAEAARK CNLDPRALES FEQHMLSDRL
     HDPVVLFHYF QIRNSICWLW IKNPTHAISR VEAQGVCVDR CLFQLASLAY EFLVRYGYIN
     YGCLSFDSSF TNETNTGTTS SSASKQKTIA VVGAGLTGLI CARQLTGLFS QYSSSFLSKN
     ELPPKVIILE AKERTGGRIY SRALPVSHTS ATQINHHTSN SNSISSNSTS LNPKDVTDPS
     HIPSAIDLGF QFLFSPMDDI LLNLLNKQLG IEVTEMTGSD LVYDETDTKV LDMVEVKKLN
     ILWEKLLEYV SVCFFINVEE SVRISWISQF QLFIDEMFPD HLSKSLSLNA SHEFSFKKTM
     LILIDEVSSY AKLGNSQKKF LIWCFKVAEL DDTLYPLNTV DTDFSKDILI PKVARRGLSQ
     LPWALQSYPS PLNIHYEKFV SKVTIENDKC TLDCKDNSSY EVDQVVIACS PSHFSSNIEF
     SPGLPNFVTE NIKSIDFKPG KKVILRYAAA FWRKNIRSFG IIPKSLSQEM NNDENDGKSC
     FVLRIWNMLP ETGVPILVAD INPQMTSSSS NETSHLIQEL HSLIVDHFQN DSNSSADLLD
     AWVTNWSRNG VYDGLNSYPN FANDKQQYEK RFRQSQLSYN LGRLHIAGDY IFSCVGCRTL
     QRSFLSGLSV CTGIIDSLAP ISLTIPIIGE TSRKELDQFL RNSKVNNFDP NAEAQRHLSY
     QARYRLKKQE RLDEHKEEQE QLVTELLGYL PEPPSKPNAN PFLLYQKMQW HVCRALADED
     KRRLTGDSTA KATINETRAK LGKTWRQLDD LGKKPWIDEI AAQREAYAGK ILRYQRLTKE
     YEMRAEQIRN DYAAKCQDEP IPDDEARLFM QAQREEEQRK QTQDDNISKS REASDEEYHD
     DGSSDSGYNG TRY
 
 
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